Article
Biotechnology & Applied Microbiology
Quang-Huy Nguyen, Duc-Hau Le
Summary: This study developed a tool called oCEM, which solves the challenges of overlap and local co-expression in co-expressed gene module detection through the use of decomposition methods and an auxiliary statistical approach. Compared to other techniques, oCEM performs better in detecting biologically relevant modules.
Article
Genetics & Heredity
Bin Li, Wen-Xuan Sun, Wan-Ying Zhang, Ye Zheng, Lu Qiao, Yue-Ming Hu, Wei-Qiang Li, Di Liu, Bing Leng, Jia-Ren Liu, Xiao-Feng Jiang, Yan Zhang
Summary: This study classified different subtypes of asthma through molecular expression analysis and identified the molecular basis associated with severe asthma. The research also revealed the association between factors such as neural signals and redox with the severity of asthma.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Tianci Song, Kathleen K. Markham, Zhuliu Li, Kristen E. Muller, Kathleen Greenham, Rui Kuang
Summary: In this article, a PPI-regularized CNN method is proposed for clustering spatial-resolved gene expression, which improves the coherence of spatial patterns and provides biological interpretation. Experimental results demonstrate that the method consistently detects gene clusters with coherent spatial patterns and significantly enriched gene functions.
Article
Mathematics, Interdisciplinary Applications
Omur Deveci, Sakine Hulku, Anthony G. Shannon
Summary: In this paper, we defined the co-complex-type k-Fibonacci numbers and explored their relationships with k-step Fibonacci numbers. Various properties of the co-complex-type k-Fibonacci numbers were produced, and the sequences were extended to groups. Finally, the periods of the co-complex-type 2-Fibonacci sequences in the semidihedral group SD2m were obtained with respect to the generating pair (x,y).
CHAOS SOLITONS & FRACTALS
(2021)
Article
Biochemical Research Methods
Chengwei Ai, Hongpeng Yang, Yijie Ding, Jijun Tang, Fei Guo
Summary: This study proposes a novel similarity-based method of low-rank matrix decomposition with multi-graph regularization to predict the associations between drugs and diseases. The experiments show that only a part of the similarity information is necessary to achieve the desired performance, and the method has advantages in evaluation measurements. Additionally, the model performs well in detecting real-world data.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Giovanni Madeo, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
Summary: Myristoylation (MYR) is a protein modification where a myristoyl group is covalently attached to a translation or after translation. SVMyr is a web server based on Support Vector Machines (SVM) that can detect both co- and post-translational myristoylation sites. The method has high scores in cross validation and outperforms other methods on experimental datasets. SVMyr can also predict post-translational myristoylation sites and confirm existing myristoylated protein sets while identifying new NMT substrates.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Computer Science, Software Engineering
Md Nadim, Manishankar Mondal, Chanchal K. Roy, Kevin A. Schneider
Summary: This study explores a dimension of code clone research for detecting cloned co-change candidates. By comparing the performance of different configurations of clone detection tools on various systems, valuable insights and guidelines are obtained for selecting and configuring clone detection tools, leading to a new approach in clone research for change impact analysis.
JOURNAL OF SYSTEMS AND SOFTWARE
(2022)
Article
Nutrition & Dietetics
Rathi Paramastri, Chien-Yeh Hsu, Yung-Kun Chuang, Hsiu-An Lee, Bayu Satria Wiratama, Jane C-J Chao
Summary: A study showed that the interaction between a liver-associated dietary pattern and unhealthy concordance lifestyle factors increases the risk of abnormal liver function. Participants with a strong liver-associated dietary pattern and unhealthy concordance lifestyles are more likely to have increased odds of abnormal liver function.
Article
Biochemical Research Methods
Yujie Wang, Gang Zhou, Tianhao Guan, Yan Wang, Chenxu Xuan, Tao Ding, Jie Gao
Summary: This study proposes a network-regularized sparse orthogonal-regularized joint non-negative matrix factorization (NSOJNMF) algorithm to explore RNA expression patterns and potential molecular mechanisms of cancer. By applying this algorithm, ceRNA co-modules of liver cancer and colon cancer are identified, and enrichment analysis shows their close association with cancer occurrence and development. In addition, potential biological associations among RNA molecules are discovered through the constructed ceRNA networks.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Microbiology
Tim J. H. Baltussen, Jordy P. M. Coolen, Paul E. Verweij, Jan Dijksterhuis, Willem J. G. Melchers
Summary: A comparative analysis of germinating Aspergillus fumigatus and A. niger conidia identified four gene modules associated with stages of germination, revealing shared biological processes between the two species. These modules were enriched with functions such as secondary metabolism, protein synthesis, protein fate, and polarized growth. The study highlights the potential of identifying potential antifungal targets through cross-species analysis.
Article
Mathematics, Applied
Maciej Wojtala
Summary: Determining the matrix multiplication exponent is a significant problem in computer science, and it remains unsolved. This study demonstrates the impossibility of proving the exponent to be 2 using fixed-degree structure tensors and arbitrary restrictions. Furthermore, it is also impossible to prove it by starting with 1(A)-generic non-diagonal tensors of fixed size with minimal border rank. This research generalizes the work of Blaser and Lysikov, incorporating methods from both commutative algebra and complexity theory.
COLLECTANEA MATHEMATICA
(2023)
Article
Biochemical Research Methods
Junrong Song, Wei Peng, Feng Wang
Summary: The heterogeneous characteristics of cancer patients present a challenge to precision medicine. Identifying cancer subtypes can improve personalized cancer medicine, future therapeutic strategies, and reduce treatment costs.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Chemistry, Multidisciplinary
Elena Galan, Andreea Raluca Hlatcu, Stefan Milicescu, Elina Teodorescu, Simina Neagoe, Ecaterina Ionescu
Summary: This research verifies the concordance between the skeletal maturity index (SMI) measured on hand and wrist X-rays using Fishman method and the cervical vertebral maturation stage (CVMS) measured on lateral cephalometric X-rays using Baccetti method. The study showed a strong correlation between the SMI and CVMS indexes within the analyzed group.
APPLIED SCIENCES-BASEL
(2022)
Article
Mathematics
Jose M. Maisog, Andrew T. DeMarco, Karthik Devarajan, Stanley Young, Paul Fogel, George Luta
Summary: Non-negative matrix factorization is a method for matrix decomposition that can be used for dimensionality reduction, but choosing the appropriate dimensionality k is crucial. Research has found that the accuracy of estimating k can be affected when the normalization method is unknown.
Article
Mathematics
The Tien Mai
Summary: This paper presents a theoretical examination of a low-rank matrix single-index model. While this model has been recently introduced in the field of biostatistics, its theoretical properties for jointly estimating the link function and the coefficient matrix have not yet been fully explored. By utilizing the PAC-Bayesian bounds technique, this paper provides a comprehensive theoretical understanding of the joint estimation process, offering valuable insights into the model's properties and potential applications in various fields.
Article
Neurosciences
Khadeejah T. Sultan, Zhi Han, Xin-Jun Zhang, Anjin Xianyu, Zhizhong Li, Kun Huang, Song-Hai Shi
Article
Neurosciences
Wei Shi, Anjin Xianyu, Zhi Han, Xing Tang, Zhizhong Li, Haining Zhong, Tianyi Mao, Kun Huang, Song-Hai Shi
NATURE NEUROSCIENCE
(2017)
Article
Multidisciplinary Sciences
Xin-Jun Zhang, Zhizhong Li, Zhi Han, Khadeejah T. Sultan, Kun Huang, Song-Hai Shi
NATURE COMMUNICATIONS
(2017)
Article
Biotechnology & Applied Microbiology
Zhi Han, Travis Johnson, Jie Zhang, Xuan Zhang, Kun Huang
BIOMED RESEARCH INTERNATIONAL
(2017)
Article
Biochemical Research Methods
Zhi Han, Lu Tian, Thierry Pecot, Tim Huang, Raghu Machiraju, Kun Huang
BMC BIOINFORMATICS
(2012)
Article
Biochemistry & Molecular Biology
Hua-Tai Xu, Zhi Han, Peng Gao, Shuijin He, Zhizhong Li, Wei Shi, Oren Kodish, Wei Shao, Keith N. Brown, Kun Huang, Song-Hai Shi
Article
Biochemistry & Molecular Biology
Peng Gao, Maria Pia Postiglione, Teresa G. Krieger, Luisirene Hernandez, Chao Wang, Zhi Han, Carmen Streicher, Ekaterina Papusheva, Ryan Insolera, Kritika Chugh, Oren Kodish, Kun Huang, Benjamin D. Simons, Liqun Luo, Simon Hippenmeyer, Song-Hai Shi
Article
Multidisciplinary Sciences
Keith N. Brown, She Chen, Zhi Han, Chun-Hui Lu, Xin Tan, Xin-Jun Zhang, Liya Ding, Alejandro Lopez-Cruz, Dieter Saur, Stewart A. Anderson, Kun Huang, Song-Hai Shi
Proceedings Paper
Computer Science, Artificial Intelligence
Fu Bo, Han Zhi, Li Zheng
PROCEEDINGS OF THE 2009 2ND INTERNATIONAL CONGRESS ON IMAGE AND SIGNAL PROCESSING, VOLS 1-9
(2009)
Article
Computer Science, Artificial Intelligence
XC Yin, CP Liu, Z Han
PATTERN RECOGNITION LETTERS
(2005)